Core biopsy rapidly replaced fine needle aspiration (FNA) over the past decade in evaluation of diseases of the female breast in many centers in the USA. We continue to heavily utilize FNA for the initial evaluation of breast masses in our institution. In this article, we discuss the cytologic and core biopsy findings in challenging breast lesions such as papillary and mucinous proliferations, fibroepithelial neoplasms, and low grade cancers. We specifically focus on the pitfalls and limitations of both diagnostic modalities in these selected specific lesions. Diagn. Cytopathol. 2012 © 2011 Wiley Periodicals, Inc.